Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2016-2018 The plumed team
       3             :    (see the PEOPLE file at the root of the distribution for a list of names)
       4             : 
       5             :    See http://www.plumed.org for more information.
       6             : 
       7             :    This file is part of plumed, version 2.
       8             : 
       9             :    plumed is free software: you can redistribute it and/or modify
      10             :    it under the terms of the GNU Lesser General Public License as published by
      11             :    the Free Software Foundation, either version 3 of the License, or
      12             :    (at your option) any later version.
      13             : 
      14             :    plumed is distributed in the hope that it will be useful,
      15             :    but WITHOUT ANY WARRANTY; without even the implied warranty of
      16             :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
      17             :    GNU Lesser General Public License for more details.
      18             : 
      19             :    You should have received a copy of the GNU Lesser General Public License
      20             :    along with plumed.  If not, see <http://www.gnu.org/licenses/>.
      21             : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
      22             : #include "core/ActionRegister.h"
      23             : #include "core/ActionShortcut.h"
      24             : #include "core/ActionWithValue.h"
      25             : #include "CoordinationNumbers.h"
      26             : #include "multicolvar/MultiColvarShortcuts.h"
      27             : #include "core/PlumedMain.h"
      28             : #include "core/ActionSet.h"
      29             : 
      30             : //+PLUMEDOC MCOLVAR TETRA_RADIAL
      31             : /*
      32             : Calculate the radial tetra CV
      33             : 
      34             : \par Examples
      35             : 
      36             : */
      37             : //+ENDPLUMEDOC
      38             : 
      39             : namespace PLMD {
      40             : namespace symfunc {
      41             : 
      42             : class RadialTetra : public ActionShortcut {
      43             : public:
      44             :   static void registerKeywords( Keywords& keys );
      45             :   explicit RadialTetra(const ActionOptions&ao);
      46             : };
      47             : 
      48             : PLUMED_REGISTER_ACTION(RadialTetra,"TETRA_RADIAL")
      49             : 
      50           3 : void RadialTetra::registerKeywords( Keywords& keys ) {
      51           3 :   CoordinationNumbers::shortcutKeywords( keys );
      52           6 :   keys.addFlag("NOPBC",false,"ignore the periodic boundary conditions when calculating distances");
      53           6 :   keys.add("compulsory","CUTOFF","-1","ignore distances that have a value larger than this cutoff");
      54           3 :   keys.remove("NN");
      55           3 :   keys.remove("MM");
      56           3 :   keys.remove("D_0");
      57           3 :   keys.remove("R_0");
      58           3 :   keys.remove("SWITCH");
      59           3 :   keys.needsAction("DISTANCE_MATRIX");
      60           3 :   keys.needsAction("NEIGHBORS");
      61           3 :   keys.needsAction("CUSTOM");
      62           3 :   keys.needsAction("ONES");
      63           3 :   keys.needsAction("MATRIX_VECTOR_PRODUCT");
      64           3 : }
      65             : 
      66           1 : RadialTetra::RadialTetra( const ActionOptions& ao):
      67             :   Action(ao),
      68           1 :   ActionShortcut(ao) {
      69             :   // Read species input and create the matrix
      70             :   bool nopbc;
      71           1 :   parseFlag("NOPBC",nopbc);
      72           1 :   std::string pbcstr="";
      73           1 :   if( nopbc ) {
      74             :     pbcstr = " NOPBC";
      75             :   }
      76             :   std::string sp_str, rcut;
      77           1 :   parse("SPECIES",sp_str);
      78           2 :   parse("CUTOFF",rcut);
      79           1 :   if( sp_str.length()>0 ) {
      80           2 :     readInputLine( getShortcutLabel() + "_mat: DISTANCE_MATRIX GROUP=" + sp_str + " CUTOFF=" + rcut + pbcstr );
      81             :   } else {
      82             :     std::string specA, specB;
      83           0 :     parse("SPECIESA",specA);
      84           0 :     parse("SPECIESB",specB);
      85           0 :     if( specA.length()==0 ) {
      86           0 :       error("missing input atoms");
      87             :     }
      88           0 :     if( specB.length()==0 ) {
      89           0 :       error("missing SPECIESB keyword");
      90             :     }
      91           0 :     readInputLine( getShortcutLabel() + "_mat: DISTANCE_MATRIX GROUPA=" + specA + " GROUPB=" + specB + " CUTOFF=" + rcut + pbcstr);
      92             :   }
      93             :   // Get the neighbors matrix
      94           2 :   readInputLine( getShortcutLabel() + "_neigh: NEIGHBORS ARG=" + getShortcutLabel() + "_mat NLOWEST=4");
      95             :   // Now get distance matrix that just contains four nearest distances
      96           2 :   readInputLine( getShortcutLabel() + "_near4: CUSTOM ARG=" + getShortcutLabel() + "_mat," + getShortcutLabel() + "_neigh FUNC=x*y PERIODIC=NO");
      97             :   //Now compute sum of four nearest distances
      98           1 :   ActionWithValue* av = plumed.getActionSet().selectWithLabel<ActionWithValue*>( getShortcutLabel() + "_mat");
      99           1 :   plumed_assert( av && av->getNumberOfComponents()>0 && (av->copyOutput(0))->getRank()==2 );
     100             :   std::string size;
     101           1 :   Tools::convert( (av->copyOutput(0))->getShape()[1], size );
     102           2 :   readInputLine( getShortcutLabel() + "_ones: ONES SIZE=" + size );
     103           2 :   readInputLine( getShortcutLabel() + "_sum4: MATRIX_VECTOR_PRODUCT ARG=" + getShortcutLabel() + "_near4," + getShortcutLabel() + "_ones");
     104             :   // Now compute squares of four nearest distance
     105           2 :   readInputLine( getShortcutLabel() + "_near4_2: CUSTOM ARG=" + getShortcutLabel() + "_near4 FUNC=x*x PERIODIC=NO");
     106             :   // Now compute sum of the squares of the four nearest distances
     107           2 :   readInputLine( getShortcutLabel() + "_sum4_2: MATRIX_VECTOR_PRODUCT ARG=" + getShortcutLabel() + "_near4_2," + getShortcutLabel() + "_ones");
     108             :   // Evaluate the average distance to the four nearest neighbors
     109           2 :   readInputLine( getShortcutLabel() + "_meanr: CUSTOM ARG=" + getShortcutLabel() + "_sum4 FUNC=0.25*x PERIODIC=NO");
     110             :   // Now evaluate the actual per atom CV
     111           2 :   readInputLine( getShortcutLabel() + ": CUSTOM ARG=" + getShortcutLabel() + "_sum4," + getShortcutLabel() + "_sum4_2," + getShortcutLabel() + "_meanr " +
     112             :                  "FUNC=(1-(y-x*z)/(12*z*z)) PERIODIC=NO");
     113             :   // And get the things to do with the quantities we have computed
     114             :   std::map<std::string,std::string> keymap;
     115           1 :   multicolvar::MultiColvarShortcuts::readShortcutKeywords( keymap, this );
     116           2 :   multicolvar::MultiColvarShortcuts::expandFunctions( getShortcutLabel(), getShortcutLabel(), "", keymap, this );
     117           1 : }
     118             : 
     119             : }
     120             : }